I have this issue now. Just did a git pull an hour ago on arcanist, libphutil and phabricator. Restarted apache and the phabricator daemons, but the warning is still there. I also did bin/phd stop and check if there were no daemons left and they were indeed all gone. There are no errors in the daemons.log file. One thing I checked is the APC cache (I have APC enabled) but its cache is cleared when Apache is restarted or reloaded. I have no idea what to do about it. Ignoring the warning doesn't feel right; it must be caused by something and that should be fixed.